BioC 3.6: CHECK report for MSnbase on veracruz1

Package: MSnbase

Version: 2.3.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MSnbase_2.3.9.tar.gz

StartedAt: 2017-08-16 05:58:57 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 06:12:18 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 800.9 seconds

RetCode: 0

Status:  OK

CheckDir: MSnbase.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MSnbase_2.3.9.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/MSnbase.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSnbase/DESCRIPTION’ ... OK
* this is package ‘MSnbase’ version ‘2.3.9’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MSnbase’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    7.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives more than one person with maintainer role:
  Laurent Gatto <lg390@cam.ac.uk> [aut, cre]
  Johannes Rainer <Johannes.Rainer@eurac.edu> [aut, cre]
  Sebastian Gibb <mail@sebastiangibb.de> [aut, cre]
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘Biobase:::.showAnnotatedDataFrame’ ‘MALDIquant:::.estimateNoise’
  ‘MALDIquant:::.localMaxima’ ‘MALDIquant:::.movingAverage’
  ‘MALDIquant:::.savitzkyGolay’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
OnDiskMSnExp-class         12.279  0.417  13.113
chromatogram-MSnExp-method  8.764  0.412  10.888
MSnSet-class                7.729  0.088   8.068
averageMSnSet               7.025  0.164   7.446
aggvar                      5.437  0.067   5.654
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/MSnbase.Rcheck/00check.log’
for details.

* installing *source* package ‘MSnbase’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c Spectrum1_class.c -o Spectrum1_class.o
Spectrum1_class.c:8:13: warning: unused function '_new_Spectrum1' [-Wunused-function]
static SEXP _new_Spectrum1(SEXP msLevel, SEXP peaksCount, SEXP rt,
            ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c Spectrum2_class.c -o Spectrum2_class.o
Spectrum2_class.c:9:13: warning: unused function '_new_Spectrum2' [-Wunused-function]
static SEXP _new_Spectrum2(SEXP msLevel, SEXP peaksCount, SEXP rt,
            ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c utils.c -o utils.o
utils.c:92:15: warning: unused variable 'ret' [-Wunused-variable]
  int i1, i2, ret;
              ^
utils.c:107:15: warning: unused variable 'ret' [-Wunused-variable]
  int i1, i2, ret;
              ^
utils.c:123:18: warning: unused variable 'ret' [-Wunused-variable]
  double d1, d2, ret;
                 ^
utils.c:133:18: warning: unused variable 'ret' [-Wunused-variable]
  double d1, d2, ret;
                 ^
utils.c:121:12: warning: unused function 'compar_double_asc_order' [-Wunused-function]
static int compar_double_asc_order(const void *p1, const void *p2)
           ^
utils.c:131:12: warning: unused function 'compar_double_desc_order' [-Wunused-function]
static int compar_double_desc_order(const void *p1, const void *p2)
           ^
6 warnings generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o MSnbase.so RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/MSnbase.Rcheck/MSnbase/libs
** R
** data
*** moving datasets to lazyload DB
Creating a new generic function for ‘smooth’ in package ‘MSnbase’
Creating a new generic function for ‘trimws’ in package ‘MSnbase’
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
** inst
** preparing package for lazy loading
Creating a new generic function for ‘smooth’ in package ‘MSnbase’
Creating a new generic function for ‘trimws’ in package ‘MSnbase’
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MSnbase)

name	user	system	elapsed
Chromatogram-class	0.084	0.002	0.086
Chromatograms-class	0.242	0.002	0.259
FeatComp-class	0.297	0.013	0.319
FeaturesOfInterest-class	0.076	0.005	0.081
MSmap-class	0.001	0.000	0.002
MSnExp-class	0.380	0.004	0.395
MSnProcess-class	0.002	0.000	0.002
MSnSet-class	7.729	0.088	8.068
MSnSetList-class	4.032	0.014	4.177
MzTab-class	1.466	0.033	4.280
NAnnotatedDataFrame-class	0.011	0.000	0.012
OnDiskMSnExp-class	12.279	0.417	13.113
ProcessingStep-class	0.007	0.000	0.007
ReporterIons-class	0.017	0.001	0.018
TMT6	0.020	0.001	0.021
addIdentificationData-methods	0.425	0.013	0.455
aggvar	5.437	0.067	5.654
averageMSnSet	7.025	0.164	7.446
bin-methods	0.457	0.017	0.483
calculateFragments-methods	0.755	0.011	0.789
chromatogram-MSnExp-method	8.764	0.412	10.888
clean-methods	0.203	0.036	0.250
combineFeatures	0.885	0.033	0.950
commonFeatureNames	0.414	0.008	0.424
compareSpectra-methods	0.214	0.005	0.222
estimateNoise-method	0.012	0.000	0.012
exprsToRatios-methods	0.091	0.001	0.104
extractPrecSpectra-methods	0.556	0.052	0.644
factorsAsStrings	0.010	0.001	0.011
featureCV	0.037	0.002	0.039
fillUp	0.015	0.000	0.018
formatRt	0.001	0.001	0.001
get.amino.acids	0.004	0.000	0.004
get.atomic.mass	0.000	0.000	0.001
getVariableName	0.003	0.000	0.003
iPQF	0.445	0.003	0.468
iTRAQ4	0.008	0.000	0.008
imageNA2	3.373	0.098	3.604
impute-methods	0.833	0.016	0.890
itraqdata	0.102	0.005	0.122
listOf	0.003	0.000	0.002
makeCamelCase	0.001	0.000	0.001
makeNaData	1.192	0.011	1.249
missing-data	3.294	0.046	3.433
mzRident2dfr	0.065	0.001	0.065
nFeatures	0.555	0.033	0.599
nQuants	0.124	0.002	0.128
naplot	0.067	0.003	0.073
navMS	1.197	0.044	1.301
normToReference	0.194	0.002	0.206
normalise-methods	0.019	0.002	0.020
npcv	0.006	0.000	0.007
pSet-class	0.003	0.001	0.003
pickPeaks-method	0.312	0.006	0.330
plot-methods	1.531	0.006	1.590
plot2d-methods	0.785	0.003	0.805
plotDensity-methods	1.204	0.005	1.240
plotMzDelta-methods	1.289	0.049	1.383
plotNA-methods	0.585	0.006	0.610
plotSpectrumSpectrum-methods	0.879	0.005	0.898
precSelection	0.024	0.001	0.025
purityCorrect-methods	0.105	0.002	0.110
quantify-methods	1.383	0.191	2.602
readMSData	1.119	0.006	1.159
readMSnSet	0.318	0.006	0.329
readMgfData	3.070	0.033	3.224
readMzIdData	2.218	0.392	2.667
readMzTabData	2.697	0.033	3.196
readMzTabData_v0.9	0.410	0.003	0.767
reduce-data.frame-method	0.006	0.000	0.006
removeNoId-methods	0.774	0.004	0.800
removePeaks-methods	0.979	0.015	1.033
removeReporters-methods	0.836	0.005	0.870
selectFeatureData	0.134	0.006	0.146
smooth-methods	0.301	0.006	0.312
trimMz-methods	0.193	0.003	0.214
writeMgfData-methods	0.001	0.001	0.002